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Something to keep in mind if parsing breaks (though we should be okay). I’m more concerned about BLAST+ XML changes...
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<div class="">chris<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"Cavanaugh, Mark (NIH/NLM/NCBI) [E]" <<a href="mailto:cavanaug@ncbi.nlm.nih.gov" class="">cavanaug@ncbi.nlm.nih.gov</a>><br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"'<a href="mailto:genbankb@net.bio.net" class="">genbankb@net.bio.net</a>' (<a href="mailto:genbankb@net.bio.net" class="">genbankb@net.bio.net</a>)"
<<a href="mailto:genbankb@magpie.bio.indiana.edu" class="">genbankb@magpie.bio.indiana.edu</a>><br class="">
</span></div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">June 26, 2015 at 5:13:50 PM CDT<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">[Genbank-bb] Change to sequence display formats : Removal of GIs by June 2016</b><br class="">
</span></div>
<br class="">
<div class="">Greetings GenBank Users,<br class="">
<br class="">
A very significant change which impacts the GenBank, GenPept, and FASTA<br class="">
display formats for sequence records at NCBI was announced in the June 2015<br class="">
GenBank release notes : The removal of GI sequence identifiers.<br class="">
<br class="">
This change could have many impacts, so it seems prudent to announce it<br class="">
independently, to ensure that as many users are aware of the change as<br class="">
possible. So Section 1.4.1 of the June release notes are reproduced below.<br class="">
<br class="">
Mark Cavanaugh<br class="">
GenBank<br class="">
NCBI/NLM/NIH/HHS<br class="">
<br class="">
<br class="">
1.4.1 GI sequence identifiers to be removed from GenBank/GenPept/FASTA formats<br class="">
<br class="">
As of 06/15/2016, the integer sequence identifiers known as "GIs" will no<br class="">
longer be included in the GenBank, GenPept, and FASTA formats supported by<br class="">
NCBI for the display of sequence records.<br class="">
<br class="">
As first described in the Release Notes for GenBank 199.0 in December 2013,<br class="">
NCBI is in the process of moving to storage solutions which utilize only<br class="">
Accession.Version identifiers. See Section 1.4.2 of these release notes for<br class="">
additional background information about those developments.<br class="">
<br class="">
Although GI sequence identifiers served their purpose well for many years,<br class="">
the Accession.Version system is completely equivalent (and much more<br class="">
human-readable).<br class="">
<br class="">
And given the shift to non-GI-based systems, the importance of using<br class="">
Accession.Version identifiers cannot be overstated. So as an initial step, NCBI<br class="">
will cease the display of GI identifiers in the flatfile and FASTA views of<br class="">
all sequence records.<br class="">
<br class="">
Previously-assigned GI identifiers will continue to exist 'behind the scenes',<br class="">
and NCBI services (including URLs, APIs, etc) which accept GIs as inputs/arguments<br class="">
will be supported, for those sequence records that have GIs, for the foreseeable<br class="">
future.<br class="">
<br class="">
Over the next year NCBI will identify all such services that do not yet<br class="">
support Accession.Version identifiers, and add that support. Users of those<br class="">
services will then be encouraged to make use of Accession.Version rather than GIs.<br class="">
Of course, for those services that already support Accession.Version, NCBI<br class="">
encourages users to begin transitioning away from GI as soon as is practical.<br class="">
<br class="">
In the sample record below, nucleotide sequence AF123456 has been assigned a<br class="">
GI of 6633795, and the protein translation of its coding region feature has<br class="">
been assigned a GI of 6633796 :<br class="">
<br class="">
LOCUS AF123456 1510 bp mRNA linear VRT 12-APR-2012<br class="">
DEFINITION Gallus gallus doublesex and mab-3 related transcription factor 1<br class="">
(DMRT1) mRNA, partial cds.<br class="">
ACCESSION AF123456<br class="">
VERSION AF123456.2 GI:6633795<br class="">
....<br class="">
CDS <1..936<br class="">
/gene="DMRT1"<br class="">
/note="cDMRT1"<br class="">
/codon_start=1<br class="">
/product="doublesex and mab-3 related transcription factor<br class="">
1"<br class="">
/protein_id="AAF19666.1"<br class="">
/db_xref="GI:6633796"<br class="">
/translation="PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSL<br class="">
IAERQRVMAVQVALRRQQAQEEELGISHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPA<br class="">
HSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSDLVVDSTYYSSFYQPSLYPYY<br class="">
NNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQWQMKGMEN<br class="">
RHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDS<br class="">
GLGCLSSSESTKGDLECEPHQEPGAFAVSPVLEGE"<br class="">
<br class="">
After June 15 2016, the GI value on the VERSION line and the GI /db_xref<br class="">
qualifier for the coding region feature will no longer be displayed:<br class="">
<br class="">
LOCUS AF123456 1510 bp mRNA linear VRT 12-APR-2012<br class="">
DEFINITION Gallus gallus doublesex and mab-3 related transcription factor 1<br class="">
(DMRT1) mRNA, partial cds.<br class="">
ACCESSION AF123456<br class="">
VERSION AF123456.2<br class="">
....<br class="">
CDS <1..936<br class="">
/gene="DMRT1"<br class="">
/note="cDMRT1"<br class="">
/codon_start=1<br class="">
/product="doublesex and mab-3 related transcription factor<br class="">
1"<br class="">
/protein_id="AAF19666.1"<br class="">
/translation="PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSL<br class="">
IAERQRVMAVQVALRRQQAQEEELGISHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPA<br class="">
HSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSDLVVDSTYYSSFYQPSLYPYY<br class="">
NNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQWQMKGMEN<br class="">
RHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDS<br class="">
GLGCLSSSESTKGDLECEPHQEPGAFAVSPVLEGE"<br class="">
<br class="">
Similarly, the GI value will be removed from the VERSION line of the GenPept<br class="">
format. Currently:<br class="">
<br class="">
LOCUS AAF19666 311 aa linear VRT 12-APR-2012<br class="">
DEFINITION doublesex and mab-3 related transcription factor 1, partial [Gallus<br class="">
gallus].<br class="">
ACCESSION AAF19666<br class="">
VERSION AAF19666.1 GI:6633796<br class="">
DBSOURCE accession AF123456.2<br class="">
....<br class="">
CDS 1..311<br class="">
/gene="DMRT1"<br class="">
/coded_by="AF123456.2:<1..936"<br class="">
<br class="">
As of 06/15/2016:<br class="">
<br class="">
LOCUS AAF19666 311 aa linear VRT 12-APR-2012<br class="">
DEFINITION doublesex and mab-3 related transcription factor 1, partial [Gallus<br class="">
gallus].<br class="">
ACCESSION AAF19666<br class="">
VERSION AAF19666.1<br class="">
DBSOURCE accession AF123456.2<br class="">
....<br class="">
CDS 1..311<br class="">
/gene="DMRT1"<br class="">
/coded_by="AF123456.2:<1..936"<br class="">
<br class="">
Note that the coding region feature for GenPept format has never included<br class="">
the display of nucleotide GI values.<br class="">
<br class="">
For FASTA format, GI values will be removed from the FASTA header/defline:<br class="">
<br class="">
Currently:<br class="">
<br class="">
<blockquote type="cite" class="">gi|6633795|gb|AF123456.2| Gallus gallus doublesex and mab-3 related transcription factor 1 (DMRT1) mRNA, partial cds<br class="">
</blockquote>
CCGGCGGCGGGCAAGAAGCTGCCGCGTCTGCCCAAGTGTGCCCGCTGCCGCAACCACGGCTACTCCTCGC<br class="">
CGCTGAAGGGGCACAAGCGGTTCTGCATGTGGCGGGACTGCCAGTGCAAGAAGTGCAGCCTGATCGCCGA<br class="">
[....]<br class="">
<br class="">
<blockquote type="cite" class="">gi|6633796|gb|AAF19666.1| doublesex and mab-3 related transcription factor 1, partial<br class="">
</blockquote>
[Gallus gallus]<br class="">
PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRRQQAQEEELGI<br class="">
SHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPAHSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSD<br class="">
LVVDSTYYSSFYQPSLYPYYNNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQ<br class="">
WQMKGMENRHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDSGLGC<br class="">
LSSSESTKGDLECEPHQEPGAFAVSPVLEGE<br class="">
<br class="">
As of 06/15/2016:<br class="">
<br class="">
<blockquote type="cite" class="">gb|AF123456.2| Gallus gallus doublesex and mab-3 related transcription factor 1 (DMRT1) mRNA, partial cds<br class="">
</blockquote>
CCGGCGGCGGGCAAGAAGCTGCCGCGTCTGCCCAAGTGTGCCCGCTGCCGCAACCACGGCTACTCCTCGC<br class="">
CGCTGAAGGGGCACAAGCGGTTCTGCATGTGGCGGGACTGCCAGTGCAAGAAGTGCAGCCTGATCGCCGA<br class="">
[....]<br class="">
<br class="">
<blockquote type="cite" class="">gb|AAF19666.1| doublesex and mab-3 related transcription factor 1, partial<br class="">
</blockquote>
[Gallus gallus]<br class="">
PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRRQQAQEEELGI<br class="">
SHPVPLPSAPEPVVKKSSSSSSCLLQDSSSPAHSTSTVAAAAASAPPEGRMLIQDIPSIPSRGHLESTSD<br class="">
LVVDSTYYSSFYQPSLYPYYNNLYNYSQYQMAVATESSSSETGGTFVGSAMKNSLRSLPATYMSSQSGKQ<br class="">
WQMKGMENRHAMSSQYRMCSYYPPTSYLGQGVGSPTCVTQILASEDTPSYSESKARVFSPPSSQDSGLGC<br class="">
LSSSESTKGDLECEPHQEPGAFAVSPVLEGE<br class="">
<br class="">
Please direct any inquiries about these changes to the NCBI Service Desk:<br class="">
<br class="">
<a href="mailto:info@ncbi.nlm.nih.gov" class="">info@ncbi.nlm.nih.gov</a><br class="">
<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
Genbankb mailing list<br class="">
<a href="mailto:Genbankb@net.bio.net" class="">Genbankb@net.bio.net</a><br class="">
http://www.bio.net/biomail/listinfo/genbankb<br class="">
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